Article ; Online: Small molecule microarrays of RNA-focused peptoids help identify inhibitors of a pathogenic group I intron.
ACS chemical biology
2009 Volume 4, Issue 4, Page(s) 299–307
Abstract: Peptoids that inhibit the group I intron RNA from Candida albicans, an opportunistic pathogen ... to identify features in the peptoids that predispose them for RNA binding. After statistical analysis ... for binding to the C. albicans group I intron ribozyme. Each ligand binder identified from microarray-based ...
| Abstract | Peptoids that inhibit the group I intron RNA from Candida albicans, an opportunistic pathogen that kills immunocompromised hosts, have been identified using microarrays. The arrayed peptoid library was constructed using submonomers with moieties similar to ones found in small molecules known to bind RNA. Library members that passed quality control analysis were spotted onto a microarray and screened for binding to the C. albicans group I intron ribozyme. Each ligand binder identified from microarray-based screening inhibited self-splicing in the presence of 1 mM nucleotide concentration of bulk yeast tRNA with IC(50)'s between 150 and 2200 microM. The binding signals and the corresponding IC(50)'s were used to identify features in the peptoids that predispose them for RNA binding. After statistical analysis of the peptoids' structures that bind, a second generation of inhibitors was constructed using these important features; all second generation inhibitors have improved potencies with IC(50)'s of <100 microM. The most potent inhibitor is composed of one phenylguanidine and three tryptamine submonomers and has an IC(50) of 31 microM. This compound is 6-fold more potent than pentamidine, a clinically used drug that inhibits self-splicing. These results show that (i) modulators of RNA function can be identified by designing RNA-focused chemical libraries and screening them via microarray; (ii) statistical analysis of ligand binders can identify features in leads that predispose them for binding to their targets; and (iii) features can then be programmed into second generation inhibitors to design ligands with improved potencies. |
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| MeSH term(s) | Animals ; Binding Sites ; Candida albicans/drug effects ; Candida albicans/enzymology ; Candida albicans/pathogenicity ; Dose-Response Relationship, Drug ; Introns/genetics ; Ligands ; Molecular Conformation ; Oligonucleotide Array Sequence Analysis/methods ; Peptide Library ; Peptoids/analogs & derivatives ; Peptoids/chemistry ; Peptoids/pharmacology ; Pneumocystis carinii/drug effects ; Pneumocystis carinii/genetics ; RNA Splicing/drug effects ; RNA, Catalytic/antagonists & inhibitors ; RNA, Catalytic/chemistry ; RNA, Catalytic/genetics ; RNA, Fungal/antagonists & inhibitors ; RNA, Fungal/chemistry ; RNA, Fungal/genetics ; RNA, Transfer/antagonists & inhibitors ; RNA, Transfer/chemistry ; RNA, Transfer/genetics ; Tetrahymena thermophila/drug effects ; Tetrahymena thermophila/genetics |
| Chemical Substances | Ligands ; Peptide Library ; Peptoids ; RNA, Catalytic ; RNA, Fungal ; RNA, Transfer (9014-25-9) |
| Language | English |
| Publishing date | 2009-03-11 |
| Publishing country | United States |
| Document type | Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't |
| ISSN | 1554-8937 |
| ISSN (online) | 1554-8937 |
| DOI | 10.1021/cb800313m |
| Database | MEDical Literature Analysis and Retrieval System OnLINE |
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